Mercurial > repos > imgteam > imagej2_find_edges
diff imagej2_noise.py @ 0:8e608a6e44ac draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 16:59:03 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_noise.py Tue Sep 17 16:59:03 2019 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python +import argparse +import os +import shutil +import subprocess +import tempfile +import imagej2_base_utils + +if __name__=="__main__": + # Parse Command Line. + parser = argparse.ArgumentParser() + parser.add_argument( '--input', dest='input', help='Path to the input file' ) + parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) + parser.add_argument( '--noise', dest='noise', help='Specified noise to add to or remove from the image' ) + parser.add_argument( '--standard_deviation', dest='standard_deviation', type=float, default=None, help='Standard deviation' ) + parser.add_argument( '--radius', dest='radius', type=float, default=None, help='Radius' ) + parser.add_argument( '--threshold', dest='threshold', type=float, default=None, help='Threshold' ) + parser.add_argument( '--which_outliers', dest='which_outliers', default=None, help='Which outliers' ) + parser.add_argument( '--randomj', dest='randomj', default=None, help='RandomJ' ) + parser.add_argument( '--trials', dest='trials', type=float, default=None, help='Trials' ) + parser.add_argument( '--probability', dest='probability', type=float, default=None, help='Probability' ) + parser.add_argument( '--lammbda', dest='lammbda', type=float, default=None, help='Lambda' ) + parser.add_argument( '--order', dest='order', type=int, default=None, help='Order' ) + parser.add_argument( '--mean', dest='mean', type=float, default=None, help='Mean' ) + parser.add_argument( '--sigma', dest='sigma', type=float, default=None, help='Sigma' ) + parser.add_argument( '--min', dest='min', type=float, default=None, help='Min' ) + parser.add_argument( '--max', dest='max', type=float, default=None, help='Max' ) + parser.add_argument( '--insertion', dest='insertion', default=None, help='Insertion' ) + parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) + parser.add_argument( '--output', dest='output', help='Path to the output file' ) + args = parser.parse_args() + + tmp_dir = imagej2_base_utils.get_temp_dir() + # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not + # work for some features. The following creates a symlink with an appropriate file + # extension that points to the Galaxy dataset. This symlink is used by ImageJ. + tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) + tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.input_datatype ) + + # Define command response buffers. + tmp_out = tempfile.NamedTemporaryFile().name + tmp_stdout = open( tmp_out, 'wb' ) + tmp_err = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_err, 'wb' ) + # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. + error_log = tempfile.NamedTemporaryFile( delete=False ).name + # Build the command line. + cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) + if cmd is None: + imagej2_base_utils.stop_err( "ImageJ not found!" ) + cmd += ' %s' % error_log + cmd += ' %s' % tmp_input_path + cmd += ' %s' % args.input_datatype + cmd += ' %s ' % args.noise + cmd += imagej2_base_utils.handle_none_type( args.standard_deviation ) + cmd += imagej2_base_utils.handle_none_type( args.radius ) + cmd += imagej2_base_utils.handle_none_type( args.threshold ) + cmd += ' %s' % args.which_outliers + cmd += ' %s' % args.randomj + cmd += imagej2_base_utils.handle_none_type( args.trials ) + cmd += imagej2_base_utils.handle_none_type( args.probability ) + cmd += imagej2_base_utils.handle_none_type( args.lammbda ) + cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' ) + cmd += imagej2_base_utils.handle_none_type( args.mean ) + cmd += imagej2_base_utils.handle_none_type( args.sigma ) + cmd += imagej2_base_utils.handle_none_type( args.min ) + cmd += imagej2_base_utils.handle_none_type( args.max ) + cmd += ' %s' % args.insertion + cmd += ' %s' % tmp_output_path + + proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) + rc = proc.wait() + + # Handle execution errors. + if rc != 0: + error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) + imagej2_base_utils.stop_err( error_message ) + # Handle processing errors. + if os.path.getsize( error_log ) > 0: + error_message = open( error_log, 'r' ).read() + imagej2_base_utils.stop_err( error_message ) + # Save the output image. + shutil.move( tmp_output_path, args.output ) + imagej2_base_utils.cleanup_before_exit( tmp_dir )